However, in some cases, accessions from one population were similar in their methylation patters to accessions from other populations.
In the only detected cases, accessions with haplotypes 2 and 9 for Tef-rht1-1 were found only with haplotypes 4 and 1, respectively, for Tef-rht1-2.
For those species for which multiple accessions were included, sequences for all accessions fell into the same clade, though in several cases accessions from multiple species grouped together with strong support (e.g. D. clintoniana and D. cristata).
In all cases, accessions with the deletion allele flowered early, with an average flowering time measured as days to flowering (DTF) of 72 in the open field experiment and 62 DTF in the greenhouse experiment.
The reason that pathology case accession numbers are challenging to remove is the wide variety of formats being used.
In this case, accessions from nearby locations were more closely related than samples from distant locations, showing geographic patterns of genetic variation probably produced by breeding and selection associated with local food preferences.
In other cases, the accession was apparently so closely related with one or more other accessions that their genotypes formed a mixed group.
In cases where accession annotations were available but the positions were not found, we performed our own BLAT searches.
The E1 gene fragments from 7 MIDV cases (GenBank accession nos. JN226792 JN226795, KF680222 KF680224) clustered with MIDV-857, differing by ≤1.2% nt and 0.5% aa levels from each other and by ≤1.4% nt and 0.6% aa levels from MIDV-857.
In the latter case, GenBank accession numbers are given.
